Deep learning in drug discovery: an integrative review and future challenges

H Askr, E Elgeldawi, H Aboul Ella… - Artificial Intelligence …, 2023 - Springer
Recently, using artificial intelligence (AI) in drug discovery has received much attention
since it significantly shortens the time and cost of developing new drugs. Deep learning (DL) …

Toward better drug discovery with knowledge graph

X Zeng, X Tu, Y Liu, X Fu, Y Su - Current opinion in structural biology, 2022 - Elsevier
Drug discovery is the process of new drug identification. This process is driven by the
increasing data from existing chemical libraries and data banks. The knowledge graph is …

On the opportunities and risks of foundation models

R Bommasani, DA Hudson, E Adeli, R Altman… - arXiv preprint arXiv …, 2021 - arxiv.org
AI is undergoing a paradigm shift with the rise of models (eg, BERT, DALL-E, GPT-3) that are
trained on broad data at scale and are adaptable to a wide range of downstream tasks. We …

Building a knowledge graph to enable precision medicine

P Chandak, K Huang, M Zitnik - Scientific Data, 2023 - nature.com
Developing personalized diagnostic strategies and targeted treatments requires a deep
understanding of disease biology and the ability to dissect the relationship between …

Utilizing graph machine learning within drug discovery and development

T Gaudelet, B Day, AR Jamasb, J Soman… - Briefings in …, 2021 - academic.oup.com
Graph machine learning (GML) is receiving growing interest within the pharmaceutical and
biotechnology industries for its ability to model biomolecular structures, the functional …

Therapeutics data commons: Machine learning datasets and tasks for drug discovery and development

K Huang, T Fu, W Gao, Y Zhao, Y Roohani… - arXiv preprint arXiv …, 2021 - arxiv.org
Therapeutics machine learning is an emerging field with incredible opportunities for
innovatiaon and impact. However, advancement in this field requires formulation of …

Network-based prediction of drug combinations

F Cheng, IA Kovács, AL Barabási - Nature communications, 2019 - nature.com
Drug combinations, offering increased therapeutic efficacy and reduced toxicity, play an
important role in treating multiple complex diseases. Yet, our ability to identify and validate …

Modeling polypharmacy side effects with graph convolutional networks

M Zitnik, M Agrawal, J Leskovec - Bioinformatics, 2018 - academic.oup.com
Motivation The use of drug combinations, termed polypharmacy, is common to treat patients
with complex diseases or co-existing conditions. However, a major consequence of …

Deep learning for healthcare: review, opportunities and challenges

R Miotto, F Wang, S Wang, X Jiang… - Briefings in …, 2018 - academic.oup.com
Gaining knowledge and actionable insights from complex, high-dimensional and
heterogeneous biomedical data remains a key challenge in transforming health care …

Biological network analysis with deep learning

G Muzio, L O'Bray, K Borgwardt - Briefings in bioinformatics, 2021 - academic.oup.com
Recent advancements in experimental high-throughput technologies have expanded the
availability and quantity of molecular data in biology. Given the importance of interactions in …